The Cancer Genome Anatomies Projects (CGAP) Genetic Annotation Initiative (GAI) is an effort to expand the collection of available gene-based genetic analysis reagents for cancer research. Its goal is to enhance the utility of information and resources generated through the NCIs CGAP in genetic studies of families and populations. High resolution genetic analysis of the human genome promises to provide important insight into common disease susceptibility. To perform such analysis will require a collection of high-throughput, high- density analysis reagents. Using informatics tools that examine redundant raw expressed sequence tag (EST) data, we have identified more than 10,000 candidate, gene-based, single nucleotide polymorphisms (SNPs). Empiric validation pilot studies indicate that greater than 75% identify common (frequency of > 1/16 chromosomes) variation. Several hundered have been tested for Mendelian transmission and placed in a genetic reference map. All of the results are distributed via the WWW and the NCBIs dbSNP. From the CGAPs WWW site (cgap.nci.nih.gov/GAI) users can perform searches, examine sequence assemblies, view the primary chromatogram data, and assess the map context of the variants. This effort has been complemented by systematic resequencing of genes of interest to cancer researchers. More than 300 3UTR regions of these genes have been forward and reversed sequenced in 8 individuals.